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mglev1n / ldscr

LD Score Regression in R
https://mglev1n.github.io/ldscr/
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Abnormal genetic correlation (rg) #15

Closed ahj-maker closed 8 months ago

ahj-maker commented 8 months ago

Dear Sir/Madam,

I am new to R and the ldscr function. I am trying to run cross-trait LDSC for two munged datasets. But I kept getting the following abnormal values:

Theoretically, the genetic correlation (rg) is between -1 and 1. However, in my results, there are some cases where rg is greater than 1 or less than -1. Is this a problem with my data or a flaw in the R package?

The data input format is as required, where dt1 and dt2 are two dataframes with 5 columns (SNP, A1, A2, N, Z):

rg_res<-ldscr::ldsc_rg( munged_sumstats = list( "liver"=dt1, "immune"=dt2), ancestry="EUR")

Please kindly advise! Thank you very much.

Best regards,

ahj

1

mglev1n commented 8 months ago

These may be relevant:

https://github.com/bulik/ldsc/issues/78 https://github.com/bulik/ldsc/issues/252

ahj-maker commented 8 months ago

Thank you for your timely response.